Question

Which of the following is untrue regarding the scoring system used in dynamic programming?

(a) If the residues are same in both the sequences the match score is assumed as +5 which is added to the diagonally positioned cell of the current cell

(b) If the residues are not same, the mismatch score is assumed as -3

(c) If the residues are not same, the mismatch score is assumed as 3

(d) The score should be added to the diagonally positioned cell of the current cell

This question was posed to me by my college director while I was bunking the class.

My enquiry is from Global Sequence Alignment in division Sequence Alignment of Bioinformatics

Answer 1

The correct choice is (c) If the residues are not same, the mismatch score is assumed as 3

The explanation is: If the residues are not same, the mismatch score is assumed as -3 and it has to be negative. However, these scores are not unique, they can be user defined also, but the mismatch and gap penalty should be the negative values.